nextflow_schema.json

{
    "$schema": "http://json-schema.org/draft-07/schema",
    "$id": "https://raw.githubusercontent.com/IARCbioinfo/RNAseq-transcript-nf/master/nextflow_schema.json",
    "title": "IARCbioinfo RNAseq-transcript-nf pipeline parameters",
    "description": "This pipeline performs transcript identification and quantification from a series of BAM files using StringTie.",
    "type": "object",
    "definitions": {
        "input_output_params": {
            "title": "Input_output_params",
            "type": "object",
            "description": "Input and output parameters",
            "default": "",
            "properties": {
                "input_folder": {
                    "type": "string",
                    "description": "Folder containing RNA-seq BAM files",
                    "default": "."
                },
                "input_file": {
                    "type": "string",
                    "description": "File in TSV format containing columns \"ID\" (sample ID), \"bam\" (path to RNA-seq BAM file), and \"readlength\" (the sample's read length)"
                },
                "readlength": {
                    "type": "integer",
                    "description": "Mean read length for count computation (only if input_folder is used)",
                    "default": 75
                },
                "output_folder": {
                    "type": "string",
                    "description": "Folder where output is written",
                    "default": "."
                }
            }
        },
        "computing_params": {
            "title": "Computing_params",
            "type": "object",
            "description": "Computing parameters",
            "default": "",
            "properties": {
                "cpu": {
                    "type": "integer",
                    "default": 2,
                    "description": "Number of CPUs used by bwa mem and sambamba"
                },
                "mem": {
                    "type": "integer",
                    "default": 2,
                    "description": "Size of memory used for mapping (in GB)"
                }
            }
        },
        "ref_params": {
            "title": "Ref_params",
            "type": "object",
            "description": "Reference parameters",
            "default": "",
            "properties": {
                "gtf": {
                    "type": "string",
                    "description": "Annotation .gtf file"
                },
                "annot_organism": {
                    "type": "string",
                    "description": "Metainformation stored in SummarizedExperiment R object",
                    "default": "Homo sapiens"
                },
                "annot_genome": {
                    "type": "string",
                    "description": "Metainformation stored in SummarizedExperiment R object",
                    "default": "Unknown"
                },
                "annot_provider": {
                    "type": "string",
                    "description": "Metainformation stored in SummarizedExperiment R object",
                    "default": "Unspecified"
                },
                "annot_version": {
                    "type": "string",
                    "description": "Metainformation stored in SummarizedExperiment R object",
                    "default": "Unspecified"
                },
                "ref": {
                    "type": "string",
                    "description": "Metainformation stored in SummarizedExperiment R object",
                    "default": "Unspecified"
                }
            },
            "required": [
                "gtf"
            ]
        },
        "pipeline_params": {
            "title": "Pipeline_params",
            "type": "object",
            "description": "Pipeline parameters",
            "default": "",
            "properties": {
                "prepDE_input": {
                    "type": "string",
                    "description": "File given to script prepDE from StringTie",
                    "default": "NO_FILE"
                },
                "twopass": {
                    "type": "boolean",
                    "description": "Enable StringTie 2-pass mode"
                },
                "help": {
                    "type": "boolean",
                    "description": "Display help"
                }
            }
        }
    },
    "allOf": [
        {
            "$ref": "#/definitions/input_output_params"
        },
        {
            "$ref": "#/definitions/computing_params"
        },
        {
            "$ref": "#/definitions/ref_params"
        },
        {
            "$ref": "#/definitions/pipeline_params"
        }
    ]
}